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- PDB-8g9m: Acinetobacter_baumannii short-chain dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8g9m
TitleAcinetobacter_baumannii short-chain dehydrogenase
ComponentsOxidoreductase, short chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase
Function / homology3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / : / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Oxidoreductase, short chain dehydrogenase/reductase family
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShaw, K. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Acinetobacter_baumannii short-chain dehydrogenase
Authors: Shaw, K. / Forwood, J.K.
History
DepositionFeb 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, short chain dehydrogenase/reductase family


Theoretical massNumber of molelcules
Total (without water)27,8041
Polymers27,8041
Non-polymers00
Water543
1
A: Oxidoreductase, short chain dehydrogenase/reductase family

A: Oxidoreductase, short chain dehydrogenase/reductase family

A: Oxidoreductase, short chain dehydrogenase/reductase family

A: Oxidoreductase, short chain dehydrogenase/reductase family


Theoretical massNumber of molelcules
Total (without water)111,2184
Polymers111,2184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area11290 Å2
ΔGint-68 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.775, 93.775, 190.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Oxidoreductase, short chain dehydrogenase/reductase family


Mass: 27804.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: fabG_3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D5YHJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 71.78 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30%(v/v) Polyethylene glycol 8,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 2.5→29.64 Å / Num. obs: 17882 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 56.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1979 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NRP

6nrp


Resolution: 2.5→29.64 Å / SU ML: 0.4227 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1524 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2652 874 4.92 %
Rwork0.2492 16881 -
obs0.25 17755 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 0 3 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211560
X-RAY DIFFRACTIONf_angle_d0.50842123
X-RAY DIFFRACTIONf_chiral_restr0.0451256
X-RAY DIFFRACTIONf_plane_restr0.0041277
X-RAY DIFFRACTIONf_dihedral_angle_d2.6957921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.49991300.43862751X-RAY DIFFRACTION99.04
2.66-2.860.3831310.36412742X-RAY DIFFRACTION99.07
2.86-3.150.31031680.31742740X-RAY DIFFRACTION98.95
3.15-3.60.27861410.26272797X-RAY DIFFRACTION99.09
3.6-4.540.24621510.21422831X-RAY DIFFRACTION99.4
4.54-29.640.21491530.20583020X-RAY DIFFRACTION99

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